AIOCG plots #57

NicolasPietteLauziere · 2021-06-17T21:27:33Z

Added AIOCG plotting capabilities

Description

Added AIOCG scatterplots capabilities

Types of changes

New feature (non-breaking change which adds functionality)

Checklist:

My code follows the code style of this project.
My change requires a change to the documentation.
I have updated the documentation accordingly.
I have added tests to cover my changes.
All new and existing tests passed.

Added AIOCG plotting capabilities

morganjwilliams

Hey @NicolasPietteLauziere!

I've added a range of comments here, some around changing a few names here and there, but largely around the 600-400 plot coordinates; I think this relates to pixels rather than the data coordinates? If so I think try to keep everything in the natural molar data coordinates and add a ax.set_aspect(4/6) within the add_to_axes(...) function - this should achieve the same effect.

Could you also add a short import in pyrolite.plot.templates.__init__.py along the lines of the following:

from .AIOCG import AIOCG

After a few changes here and there this should be ready to merge. If you get stuck with any of the suggestions or have any questions feel free to ping me! If needed I can also make changes after merging into develop to round it off.

pyrolite/geochem/alteration.py

pyrolite/plot/templates/AIOCG.py

morganjwilliams · 2021-06-21T04:21:44Z

pyrolite/util/classification.py

+                if cfg["poly"]:
+                    verts = np.array(cfg["poly"]) * rescale_by
+                    x, y = get_centroid(matplotlib.patches.Polygon(verts))
+                    label = cfg["name"][0]


For things which don't have names, you can leave the annotation step out:

if label: ax.annotate( ... )

pyrolite/util/classification.py

morganjwilliams · 2021-06-21T04:29:14Z

pyrolite/util/classification.py

+            Whether to fill the polygons.
+        axes_scale : :class:`float`
+            Maximum scale for the axes. Typically 100 (for wt%) or 1 (fractional).
+        labels : :class:`str`


I don't think this classifier has different sets of labels, so if you do accept the labels kwarg, there should be a logger.info(...) or that it doesn't do anything, and generally I'd remove it from the docstring.

morganjwilliams · 2021-06-21T04:29:59Z

pyrolite/util/classification.py

+            Axis to add the polygons to.
+        fill : :class:`bool`
+            Whether to fill the polygons.
+        axes_scale : :class:`float`


I think the default scale for this is 1.0; and then you'll want to set the aspect of the Axes to 6:4?

morganjwilliams · 2021-06-21T04:31:22Z

pyrolite/data/models/AIOCG/config.json

@@ -0,0 +1 @@
+{"name":"AIOCG","axes":{"x":"(2Ca+5Fe+2Mn)+(2Ca+5Fe+2Mn+Mg+Si) molar","y":"K/(K+Na+0.5Ca) molar"},"fields":{"K":{"name":["K"],"poly":[[0,405.2],[103.2,405.2],[109.4,244.1],[51.6,235.0],[39.6,222.8],[45.6,194.4],[0,194.4]]},"KintNa":{"name":[""],"poly":[[0,194.4],[0,121.5],[145.7,121.5],[54.7,176.2],[45.6,194.4]]},"Na":{"name":["Na"],"poly":[[0,121.5],[145.7,121.5],[145.7,32.4],[157.9,0.0],[0,0.0]]},"NotAltered1":{"name":[""],"poly":[[291.6,145.9],[221.7,72.5],[294.7,30.5],[346.3,44.6],[352.3,54.7],[346.3,73.0],[334.1,101.3],[315.8,117.6]]},"NotAltered2":{"name":[""],"poly":[[291.6,145.9],[221.7,72.5],[294.7,30.5],[346.3,44.6],[352.3,54.7],[346.3,73.0],[334.1,101.3],[315.8,117.6]]},"Na-Ca-Fe-(Mg)":{"name":["Na-Ca-Fe-(Mg)"],"poly":[[145.7,121.5],[145.7,32.4],[157.9,0.0],[413,0.0],[400.8,48.7],[367.4,77.1],[352.3,117.6],[315.8,117.6],[334.1,101.3],[346.3,73.0],[352.3,54.7],[346.3,44.6],[294.7,30.5],[206.6,81.1]]},"KintK-Fe":{"name":[""],"poly":[[103.2,405.2],[109.4,244.1],[115.4,245.1],[197.5,223.5],[200.4,275.6],[194.4,405.2]]},"K-Fe":{"name":["K-Fe"],"poly":[[194.4,405.2],[200.4,275.6],[197.5,223.5],[200.4,222.8],[437.2,222.8],[431.2,328.1],[413,364.6],[413,405.2]]},"Ca-K-Fe":{"name":["Ca-K-Fe"],"poly":[[200.4,222.8],[291.6,145.9],[315.8,117.6],[352.3,117.6],[443.5,117.6],[437.2,222.8]]},"Ca-Fe-(Mg)":{"name":["Ca-Fe-(Mg)"],"poly":[[352.3,117.6],[367.4,77.1],[400.8,48.7],[413,0.0],[461.7,0.0],[445.4,70.8],[443.5,117.6]]},"Fe-rich_Ca-Fe":{"name":["Fe-rich Ca-Fe"],"poly":[[443.5,117.6],[445.4,70.8],[461.7,0.0],[607.4,0.0],[607.4,117.6]]},"Fe-rich_Ca-K-Fe":{"name":["Fe-rich Ca-K-Fe"],"poly":[[437.2,222.8],[443.5,117.6],[607.4,117.6],[607.4,222.8]]},"Fe-rich_K-Fe":{"name":["Fe-rich K-Fe"],"poly":[[413,405.2],[413,364.6],[431.2,328.1],[437.2,222.8],[607.4,222.8],[607.4,405.2]]}}}


A quick question about these coordinates - are they in pixels? It would be good to convert them back to molar proportions if so, and then just set the aspect of the axes on which the diagram is plotted to the 6-4 ratio which it's typically found in.

morganjwilliams · 2021-06-21T04:32:50Z

pyrolite/util/classification.py

+
+        with open(src, "r") as f:
+            config = json.load(f)
+        kw = dict(scale=100.0, xlim=[0, 607.4], ylim=[0, 405.2])


I think the scale should be 1.0 here; and if data coordinates (0-1) are separated from the plot aspect (6:4), the limits should both be (0, 1).

morganjwilliams · 2021-06-21T04:39:12Z

pyrolite/util/classification.py

+                    # )
+
+
+        ax.set_ylabel("$K/(K+Na+0.5Ca) molar$")


I think you can probably leave out the molar in the plot axes labels, or at least move it outside the $mathtext$ section so it's rendered as standard text.

morganjwilliams · 2021-07-05T08:21:04Z

Hey @NicolasPietteLauziere, just giving this one a bump. Let me know if you're happy to (and have time) to make these changes to your AIOCG plot before I merge it in. Cheers!

NicolasPietteLauziere · 2021-07-08T15:43:20Z

Hi Morgan, I'm happy to do the changes. It will take me a bit of time to do it as I am finishing my thesis final chapter (!!!).

Edits following Owner's comments. Not stable yet.

morganjwilliams · 2021-07-08T23:01:19Z

@NicolasPietteLauziere, no worries! Good luck with the writing up in the meantime! 😄

I'll update the target release for this one to v0.3.2.

NicolasPietteLauziere added 2 commits June 17, 2021 14:24

AIOCG plots

b294f11

Added AIOCG plotting capabilities

Update config.json

b6a06b2

morganjwilliams self-requested a review June 21, 2021 03:58

morganjwilliams added the enhancement New feature or request label Jun 21, 2021

morganjwilliams added this to the 0.3.1 milestone Jun 21, 2021

morganjwilliams reviewed Jun 21, 2021

View reviewed changes

Edits

20fbb03

Edits following Owner's comments. Not stable yet.

morganjwilliams modified the milestones: 0.3.1, 0.3.2 Jul 8, 2021

Fixing errors

97a57bc

morganjwilliams modified the milestones: 0.3.2, 0.3.3 Jul 8, 2022

morganjwilliams force-pushed the develop branch from 24b326c to 202edc7 Compare July 4, 2023 04:09

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AIOCG plots #57

AIOCG plots #57

NicolasPietteLauziere commented Jun 17, 2021 •

edited by morganjwilliams

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NicolasPietteLauziere commented Jul 8, 2021

morganjwilliams commented Jul 8, 2021

		@@ -0,0 +1 @@
		{"name":"AIOCG","axes":{"x":"(2Ca+5Fe+2Mn)+(2Ca+5Fe+2Mn+Mg+Si) molar","y":"K/(K+Na+0.5Ca) molar"},"fields":{"K":{"name":["K"],"poly":[[0,405.2],[103.2,405.2],[109.4,244.1],[51.6,235.0],[39.6,222.8],[45.6,194.4],[0,194.4]]},"KintNa":{"name":[""],"poly":[[0,194.4],[0,121.5],[145.7,121.5],[54.7,176.2],[45.6,194.4]]},"Na":{"name":["Na"],"poly":[[0,121.5],[145.7,121.5],[145.7,32.4],[157.9,0.0],[0,0.0]]},"NotAltered1":{"name":[""],"poly":[[291.6,145.9],[221.7,72.5],[294.7,30.5],[346.3,44.6],[352.3,54.7],[346.3,73.0],[334.1,101.3],[315.8,117.6]]},"NotAltered2":{"name":[""],"poly":[[291.6,145.9],[221.7,72.5],[294.7,30.5],[346.3,44.6],[352.3,54.7],[346.3,73.0],[334.1,101.3],[315.8,117.6]]},"Na-Ca-Fe-(Mg)":{"name":["Na-Ca-Fe-(Mg)"],"poly":[[145.7,121.5],[145.7,32.4],[157.9,0.0],[413,0.0],[400.8,48.7],[367.4,77.1],[352.3,117.6],[315.8,117.6],[334.1,101.3],[346.3,73.0],[352.3,54.7],[346.3,44.6],[294.7,30.5],[206.6,81.1]]},"KintK-Fe":{"name":[""],"poly":[[103.2,405.2],[109.4,244.1],[115.4,245.1],[197.5,223.5],[200.4,275.6],[194.4,405.2]]},"K-Fe":{"name":["K-Fe"],"poly":[[194.4,405.2],[200.4,275.6],[197.5,223.5],[200.4,222.8],[437.2,222.8],[431.2,328.1],[413,364.6],[413,405.2]]},"Ca-K-Fe":{"name":["Ca-K-Fe"],"poly":[[200.4,222.8],[291.6,145.9],[315.8,117.6],[352.3,117.6],[443.5,117.6],[437.2,222.8]]},"Ca-Fe-(Mg)":{"name":["Ca-Fe-(Mg)"],"poly":[[352.3,117.6],[367.4,77.1],[400.8,48.7],[413,0.0],[461.7,0.0],[445.4,70.8],[443.5,117.6]]},"Fe-rich_Ca-Fe":{"name":["Fe-rich Ca-Fe"],"poly":[[443.5,117.6],[445.4,70.8],[461.7,0.0],[607.4,0.0],[607.4,117.6]]},"Fe-rich_Ca-K-Fe":{"name":["Fe-rich Ca-K-Fe"],"poly":[[437.2,222.8],[443.5,117.6],[607.4,117.6],[607.4,222.8]]},"Fe-rich_K-Fe":{"name":["Fe-rich K-Fe"],"poly":[[413,405.2],[413,364.6],[431.2,328.1],[437.2,222.8],[607.4,222.8],[607.4,405.2]]}}}

AIOCG plots #57

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AIOCG plots #57

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NicolasPietteLauziere commented Jun 17, 2021 •

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